538 | Nature | Vol 582 | 25 June 2020
Article
preferentially expressed in state 3, 13 are endosymbiotic markers that
are expressed at higher levels in the FACS-isolated alga-containing
Xenia cells than that in the alga-free cells. By contrast, none of the genes
preferentially expressed in state 5 is an endosymbiotic marker. Instead,
state-5 cells preferentially express several oxidative-stress-response
genes (see Supplementary Table 6 for detailed descriptions). Because
increased oxidative stress is observed upon cellular ageing and during
coral bleaching^33 –^35 , state-5 cells may represent a natural ageing state
of endosymbiotic cells that are no longer able to hold on to their algae.
Additional molecular studies exploring the function of the differen-
tially expressed genes in each state are needed to further validate our
five-state hypothesis.
Summary and outlook
Here we demonstrate the power of genomic and bioinformatic tools
in studying coral biology. The Xenia sp. genome encodes essen-
tial components of RNA interference, such as Dicer and Ago, and
DNA repair pathway proteins, which should enable the development
of gene-manipulation tools to determine the mechanism of endos-
ymbiosis. Although we focused on studying the endosymbiotic cell
lineage, the regenerative processes for the other cell clusters can
be similarly investigated in future analyses. Our studies suggest
that Xenia endosymbiotic cells exist in five progressive states that
are dynamic between homeostatic conditions and the regeneration
process (Fig. 4f). It will be important to further understand the endo-
symbiotic lineage progression under different environmental stress-
ors and to test whether efficient recovery from bleaching relies on
state-1 pre-endosymbiotic cells. It is also feasible to test whether forced
regeneration by fragmenting bleached corals can stimulate the expan-
sion of state-1 pre-endosymbiotic cells and the restoration of endos-
ymbiosis.
Online content
Any methods, additional references, Nature Research reporting sum-
maries, source data, extended data, supplementary information,
acknowledgements, peer review information; details of author con-
tributions and competing interests; and statements of data and code
availability are available at https://doi.org/10.1038/s41586-020-2385-7.
- Davy, S. K., Allemand, D. & Weis, V. M. Cell biology of cnidarian–dinoflagellate symbiosis.
Microbiol. Mol. Biol. Rev. 76 , 229–261 (2012). - Putnam, H. M., Barott, K. L., Ainsworth, T. D. & Gates, R. D. The vulnerability and resilience
of reef-building corals. Curr. Biol. 27 , R528–R540 (2017). - McFadden, C. S., Reynolds, A. M. & Janes, M. P. DNA barcoding of xeniid soft corals
(Octocorallia: Alcyonacea: Xeniidae) from Indonesia: species richness and phylogenetic
relationships. Syst. Biodivers. 12 , 247–257 (2014). - Sproles, A. E. et al. Phylogenetic characterization of transporter proteins in the cnidarian–
dinoflagellate symbiosis. Mol. Phylogenet. Evol. 120 , 307–320 (2018). - Matthews, J. L. et al. Optimal nutrient exchange and immune responses operate in
partner specificity in the cnidarian–dinoflagellate symbiosis. Proc. Natl Acad. Sci. USA
114 , 13194–13199 (2017). - Yuyama, I., Ishikawa, M., Nozawa, M., Yoshida, M. A. & Ikeo, K. Transcriptomic changes
with increasing algal symbiont reveal the detailed process underlying establishment of
coral–algal symbiosis. Sci. Rep. 8 , 16802 (2018). - Pinzón, J. H. et al. Whole transcriptome analysis reveals changes in expression of
immune-related genes during and after bleaching in a reef-building coral. R. Soc. Open
Sci. 2 , 140214 (2015). - Wolfowicz, I. et al. Aiptasia sp. larvae as a model to reveal mechanisms of symbiont
selection in cnidarians. Sci. Rep. 6 , 32366 (2016). - Lehnert, E. M. et al. Extensive differences in gene expression between symbiotic and
aposymbiotic cnidarians. G3 (Bethesda) 4 , 277–295 (2014).
10. Neubauer, E. F. et al. A diverse host thrombospondin-type-1 repeat protein repertoire
promotes symbiont colonization during establishment of cnidarian–dinoflagellate
symbiosis. eLife 6 , e24494 (2017).
11. Neubauer, E. F., Poole, A. Z., Weis, V. M. & Davy, S. K. The scavenger receptor repertoire in
six cnidarian species and its putative role in cnidarian–dinoflagellate symbiosis. PeerJ 4 ,
e2692 (2016).
12. Wood-Charlson, E. M., Hollingsworth, L. L., Krupp, D. A. & Weis, V. M. Lectin/glycan
interactions play a role in recognition in a coral/dinoflagellate symbiosis. Cell. Microbiol.
8 , 1985–1993 (2006).
13. Zheng, X. et al. Lamins organize the global three-dimensional genome from the nuclear
periphery. Mol. Cell 71 , 802–815 (2018).
14. Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields
chromosome-length scaffolds. Science 356 , 92–95 (2017).
15. Kayal, E. et al. Phylogenomics provides a robust topology of the major cnidarian lineages
and insights on the origins of key organismal traits. BMC Evol. Biol. 18 , 68–86 (2018).
16. Chen, G., Ning, B. & Shi, T. Single-cell RNA-seq technologies and related computational
data analysis. Front. Genet. 10 , 317 (2019).
17. Herring, C. A., Chen, B., McKinley, E. T. & Lau, K. S. Single-cell computational strategies
for lineage reconstruction in tissue systems. Cell. Mol. Gastroenterol. Hepatol. 5 ,
539–548 (2018).
18. Sebe-Pedros, A. et al. Cnidarian cell type diversity and regulation revealed by
whole-organism single-cell RNA-seq. Cell 173 , 1520–1534 (2018).
19. Hwang, J. S. et al. Nematogalectin, a nematocyst protein with GlyXY and galectin
domains, demonstrates nematocyte-specific alternative splicing in Hydra. Proc. Natl
Acad. Sci. USA 107 , 18539–18544 (2010).
20. David, C. N. et al. Evolution of complex structures: minicollagens shape the cnidarian
nematocyst. Trends Genet. 24 , 431–438 (2008).
21. Silverstein, R. L., Li, W., Park, Y. M. & Rahaman, S. O. Mechanisms of cell signaling by the
scavenger receptor CD36: implications in atherosclerosis and thrombosis. Trans. Am.
Clin. Climatol. Assoc. 121 , 206–220 (2010).
22. Kang, W. & Reid, K. B. DMBT1, a regulator of mucosal homeostasis through the linking of
mucosal defense and regeneration? FEBS Lett. 540 , 21–25 (2003).
23. End, C. et al. DMBT1 functions as pattern-recognition molecule for poly-sulfated and
poly-phosphorylated ligands. Eur. J. Immunol. 39 , 833–842 (2009).
24. Cenik, B., Sephton, C. F., Kutluk Cenik, B., Herz, J. & Yu, G. Progranulin: a proteolytically
processed protein at the crossroads of inflammation and neurodegeneration. J. Biol.
Chem. 287 , 32298–32306 (2012).
25. Popov, I. K., Ray, H. J., Skoglund, P., Keller, R. & Chang, C. The RhoGEF protein Plekhg5
regulates apical constriction of bottle cells during gastrulation. Development 145 ,
dev168922 (2018).
26. Meyer, E. & Weis, V. M. Study of cnidarian–algal symbiosis in the “omics” age. Biol. Bull.
223 , 44–65 (2012).
27. Barott, K. L., Venn, A. A., Perez, S. O., Tambutté, S. & Tresguerres, M. Coral host cells
acidify symbiotic algal microenvironment to promote photosynthesis. Proc. Natl Acad.
Sci. USA 112 , 607–612 (2015).
28. Alessandrini, F., Pezzè, L. & Ciribilli, Y. LAMPs: shedding light on cancer biology. Semin.
Oncol. 44 , 239–253 (2017).
29. Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by
pseudotemporal ordering of single cells. Nat. Biotechnol. 32 , 381–386 (2014).
30. La Manno, G. et al. RNA velocity of single cells. Nature 560 , 494–498 (2018).
31. Afelik, S., Pool, B., Schmerr, M., Penton, C. & Jensen, J. Wnt7b is required for epithelial
progenitor growth and operates during epithelial-to-mesenchymal signaling in
pancreatic development. Dev. Biol. 399 , 204–217 (2015).
32. O’Brien, L. L. et al. Wnt11 directs nephron progenitor polarity and motile behavior
ultimately determining nephron endowment. eLife 7 , e40392 (2018).
33. Downs, C. A. et al. Oxidative stress and seasonal coral bleaching. Free Radic. Biol. Med.
33 , 533–543 (2002).
34. Mydlarz, L. D. & Jacobs, R. S. An inducible release of reactive oxygen radicals in four
species of gorgonian corals. Mar. Freshwat. Behav. Physiol. 39 , 143–152 (2006).
35. Finkel, T. & Holbrook, N. J. Oxidants, oxidative stress and the biology of ageing. Nature
408 , 239–247 (2000).
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations.Open Access This article is licensed under a Creative Commons Attribution
4.0 International License, which permits use, sharing, adaptation, distribution
and reproduction in any medium or format, as long as you give appropriate
credit to the original author(s) and the source, provide a link to the Creative Commons license,
and indicate if changes were made. The images or other third party material in this article are
included in the article’s Creative Commons license, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons license and your
intended use is not permitted by statutory regulation or exceeds the permitted use, you will
need to obtain permission directly from the copyright holder. To view a copy of this license,
visit http://creativecommons.org/licenses/by/4.0/.© The Author(s) 2020